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Release v0.5.2
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Merge pull request #1406 from ICB-DCM/develop
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PaulJonasJost authored May 31, 2024
2 parents d8333bd + c966568 commit d38005e
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51 changes: 25 additions & 26 deletions .github/workflows/ci.yml
Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ['3.9', '3.11']
python-version: ['3.10', '3.12']

steps:
- name: Check out repository
Expand All @@ -41,7 +41,7 @@ jobs:
path: |
~/.cache/pip
.tox/
key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}
key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"

- name: Install dependencies
run: .github/workflows/install_deps.sh amici
Expand All @@ -60,10 +60,10 @@ jobs:
file: ./coverage.xml

mac:
runs-on: macos-latest
runs-on: macos-13 # TODO: change to macos-latest after the next release
strategy:
matrix:
python-version: ['3.11']
python-version: ['3.12']

steps:
- name: Check out repository
Expand All @@ -80,14 +80,14 @@ jobs:
path: |
~/.cache/pip
.tox/
key: ${{ runner.os }}-${{ matrix.python-version }}-ci
key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"

- name: Install dependencies
run: .github/workflows/install_deps.sh amici

- name: Run tests
timeout-minutes: 30
run: tox -e base
run: ulimit -n 65536 65536 && tox -e base

- name: Coverage
uses: codecov/codecov-action@v3
Expand All @@ -99,7 +99,7 @@ jobs:
runs-on: windows-latest
strategy:
matrix:
python-version: ['3.11']
python-version: ['3.12']

steps:
- name: Check out repository
Expand All @@ -116,7 +116,7 @@ jobs:
path: |
~\AppData\Local\pip\Cache
.tox
key: ${{ runner.os }}-${{ matrix.python-version }}-ci
key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"

- name: Install dependencies
run: |
Expand All @@ -132,7 +132,7 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ['3.9', '3.11']
python-version: ['3.10', '3.12']

steps:
- name: Check out repository
Expand All @@ -149,7 +149,7 @@ jobs:
path: |
~/.cache/pip
.tox/
key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}
key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"

- name: Install dependencies
run: .github/workflows/install_deps.sh amici pysb
Expand All @@ -171,7 +171,7 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ['3.9', '3.11']
python-version: ['3.10', '3.12']

# needed to allow julia-actions/cache to delete old caches that it has created
permissions:
Expand All @@ -193,7 +193,7 @@ jobs:
path: |
~/.cache/pip
.tox/
key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}
key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"

- name: Install julia
uses: julia-actions/setup-julia@v1
Expand Down Expand Up @@ -225,8 +225,7 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
# ipopt does not work on 3.9 (https://github.com/mechmotum/cyipopt/issues/225)
python-version: ['3.11']
python-version: ['3.12']

steps:
- name: Check out repository
Expand All @@ -243,7 +242,7 @@ jobs:
path: |
~/.cache/pip
.tox/
key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}
key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"

- name: Install dependencies
run: .github/workflows/install_deps.sh ipopt
Expand All @@ -262,7 +261,7 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ['3.9', '3.11']
python-version: ['3.10', '3.12']

steps:
- name: Check out repository
Expand All @@ -279,7 +278,7 @@ jobs:
path: |
~/.cache/pip
.tox/
key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}
key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"

- name: Install dependencies
run: .github/workflows/install_deps.sh amici
Expand All @@ -298,7 +297,7 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ['3.9', '3.11']
python-version: ['3.10', '3.12']

steps:
- name: Check out repository
Expand All @@ -315,7 +314,7 @@ jobs:
path: |
~/.cache/pip
.tox/
key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}
key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"

- name: Install dependencies
run: .github/workflows/install_deps.sh amici
Expand All @@ -334,7 +333,7 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ['3.11']
python-version: ['3.12']

steps:
- name: Check out repository
Expand All @@ -351,7 +350,7 @@ jobs:
path: |
~/.cache/pip
.tox/
key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}
key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"

- name: Install dependencies
run: pip install tox pre-commit
Expand Down Expand Up @@ -383,7 +382,7 @@ jobs:
path: |
~/.cache/pip
.tox/
key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}
key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"

- name: Install dependencies
run: .github/workflows/install_deps.sh doc amici
Expand All @@ -399,7 +398,7 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ['3.9']
python-version: ['3.10']

steps:
- name: Check out repository
Expand All @@ -416,7 +415,7 @@ jobs:
path: |
~/.cache/pip
.tox/
key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}
key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"

- name: Install dependencies
run: .github/workflows/install_deps.sh amici ipopt
Expand All @@ -429,7 +428,7 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ['3.9']
python-version: ['3.10']

steps:
- name: Check out repository
Expand All @@ -446,7 +445,7 @@ jobs:
path: |
~/.cache/pip
.tox/
key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}
key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"

- name: Install dependencies
run: .github/workflows/install_deps.sh amici
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/deploy.yml
Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ['3.9']
python-version: ['3.12']

steps:
- name: Check out repository
Expand Down
31 changes: 31 additions & 0 deletions CHANGELOG.rst
Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,37 @@ Release notes
..........


0.5.2 (2024-05-27)
-------------------

* **New Feature**: Variational inference with PyMC (#1306)
* PEtab
* Import of petab independent of amici (#1355)
* Problem
* Added option to sample startpoints for a problem, from the problem directly. (#1364)
* More detailed defaults for problem.get_full_vector (#1393)
* Save pypesto and python version to the problem. (#1382)
* Objective
* Fix calling priors in sampling with fixed parameters (#1378)
* Fix JaxObjective (#1400)
* Optimize
* ESS optimizers: suppress divide-by-zero warnings; report n_eval (#1380)
* SacessOptimizer: collect worker stats (#1381)
* Add load method to Hdf5AmiciHistory (#1370)
* Hierarchical
* Relative: fix log of zero for default 0 sigma values (#1377)
* Sample
* Fix pypesto.sample.geweke_test.spectrum for nfft<=3 (#1388)
* Visualize
* Handle correlation plot with nans (#1365)
* General
* Remove scipy requirement from pypesto[pymc] (#1376)
* Require and test python >=3.10 according to NEP 29 (#1379)
* Fix various warnings (#1384)
* Small changes to GHA actions and tests (#1386, #1387, #1402, #1385)
* Improve Documentation (#1394, #1391, #1399, #1292, #1390)


0.5.0 (2024-04-10)
-------------------

Expand Down
9 changes: 6 additions & 3 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -25,12 +25,15 @@ pyPESTO features include:
* Parameter estimation pipeline for systems biology problems specified in
[SBML](http://sbml.org/) and [PEtab](https://github.com/PEtab-dev/PEtab)
([example](https://github.com/ICB-DCM/pyPESTO/blob/master/doc/example/petab_import.ipynb))
* Parameter estimation with relative (scaled and offset) data as described in
[Schmiester et al. (2020)](https://doi.org/10.1093/bioinformatics/btz581).
([example](https://github.com/ICB-DCM/pyPESTO/blob/master/doc/example/relative_data.ipynb))
* Parameter estimation with ordinal data as described in
[Schmiester et al. (2020)](https://doi.org/10.1007/s00285-020-01522-w) and
[Schmiester et al. (2021)](https://doi.org/10.1093/bioinformatics/btab512).
([example](https://github.com/ICB-DCM/pyPESTO/blob/master/doc/example/ordinal.ipynb))
* Parameter estimation with censored data. ([example](https://github.com/ICB-DCM/pyPESTO/blob/master/doc/example/censored.ipynb))
* Parameter estimation with nonlinear-monotone data. ([example](https://github.com/ICB-DCM/pyPESTO/blob/master/doc/example/nonlinear_monotone.ipynb))
([example](https://github.com/ICB-DCM/pyPESTO/blob/master/doc/example/ordinal_data.ipynb))
* Parameter estimation with censored data. ([example](https://github.com/ICB-DCM/pyPESTO/blob/master/doc/example/censored_data.ipynb))
* Parameter estimation with nonlinear-monotone data. ([example](https://github.com/ICB-DCM/pyPESTO/blob/master/doc/example/semiquantitative_data.ipynb))

## Quick install

Expand Down
6 changes: 2 additions & 4 deletions doc/example/amici.ipynb
Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,6 @@
"source": [
"# import\n",
"import logging\n",
"import random\n",
"import tempfile\n",
"from pprint import pprint\n",
"\n",
Expand All @@ -57,7 +56,8 @@
"mpl.rcParams[\"figure.dpi\"] = 100\n",
"mpl.rcParams[\"font.size\"] = 18\n",
"\n",
"random.seed(1912)\n",
"# Set seed for reproducibility\n",
"np.random.seed(1912)\n",
"\n",
"\n",
"# name of the model that will also be the name of the python module\n",
Expand Down Expand Up @@ -929,8 +929,6 @@
"outputs": [],
"source": [
"%%time\n",
"# Set seed for reproducibility\n",
"np.random.seed(1)\n",
"result = optimize.minimize(\n",
" problem=problem,\n",
" optimizer=optimizer,\n",
Expand Down
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